def test_OPLS_method(self):
"""It tests the OPLS method"""
ligand_path = get_data_file_path(self.LIGAND_PATH)
molecule = Molecule(ligand_path)
# To avoid the use of Schrodinger Toolkit
charges = [-0.22, 0.7, -0.12, -0.8, -0.8, -0.12, -0.12, -0.12,
-0.12, -0.12, -0.115, -0.115, -0.12, -0.12, -0.12,
-0.12, -0.12, -0.12, -0.12, -0.18, 0.06, 0.06, 0.06,
0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06,
0.06, 0.06, 0.115, 0.115, 0.06, 0.06, 0.06, 0.06, 0.06,
0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06,
0.06, 0.06, 0.06]
molecule._OPLS_parameters = SchrodingerToolkitWrapper.OPLSParameters(
{'charges': [unit.Quantity(charge, unit.elementary_charge)
for charge in charges]})
molecule.parameterize(FORCEFIELD_NAME, charges_method='OPLS')
assert len(molecule.off_molecule.partial_charges) == len(charges), \
'Size of Molecule\'s partial charges is expected to match ' \
+ 'with size of reference charges list'
for charge, expected_charge in zip(
molecule.off_molecule.partial_charges, charges):
assert charge == unit.Quantity(expected_charge,
unit.elementary_charge), \
'Unexpected charge {}'.format(charge)
def test_get_Schrodinger_parameters(self):
"""
It tests the standard methods to obtain Schrodinger parameters
from an offpele's Molecule.
"""
# Load benzene ring
molecule = Molecule(smiles='c1ccccc1')
molecule.parameterize(FORCEFIELD_NAME, charges_method='gasteiger')
with pytest.raises(ToolkitUnavailableException):
molecule.get_OPLS_parameters()
molecule._OPLS_parameters = METHANE_OPLS_PARAMETERS
_ = molecule.get_OPLS_parameters()
molecule.add_OPLS_nonbonding_params()
molecule.add_OPLS_bonds_and_angles()
def test_assign_Schrodinger_parameters(self):
"""
It tests the assignment of Schrodinger parameters to offpele's
Molecule.
"""
def check_parameters():
""" It checks the current parameters of the molecule. """
for atom in molecule.atoms:
w_atom = WritableAtom(atom)
w_parameters = [
w_atom.index, w_atom.parent.index, w_atom.core,
w_atom.OPLS_type, w_atom.PDB_name, w_atom.unknown,
w_atom.sigma, w_atom.epsilon, w_atom.charge,
w_atom.born_radius, w_atom.SASA_radius,
w_atom.nonpolar_gamma, w_atom.nonpolar_alpha
]
assert w_parameters in expected_nonbonding, \
'Invalid writable nonbonding parameters {}'.format(w_parameters)
for bond in molecule.bonds:
w_bond = WritableBond(bond)
w_parameters = [attr[1] for attr in list(w_bond)]
assert w_parameters in expected_bonds, \
'Invalid writable bond parameters {}'.format(w_parameters)
for angle in molecule.angles:
w_angle = WritableAngle(angle)
w_parameters = [attr[1] for attr in list(w_angle)]
assert w_parameters in expected_angles, \
'Invalid writable angle parameters {}'.format(w_parameters)
# Load benzene ring
molecule = Molecule(smiles='C')
molecule.parameterize(FORCEFIELD_NAME)
# Load OPLS parameters
molecule._OPLS_parameters = METHANE_OPLS_PARAMETERS
# Check parameters
# First check
expected_nonbonding = [[
1, 0, 'M', 'OFFT', '_C1_', 0, 3.3996695084235347, 0.1094, -0.1088,
0, 1.6998347542117673, 0, 0
],
[
2, 1, 'M', 'OFFT', '_H1_', 0,
2.649532787749369, 0.0157, 0.0267, 0,
1.3247663938746845, 0, 0
],
[
3, 1, 'M', 'OFFT', '_H2_', 0,
2.649532787749369, 0.0157, 0.0267, 0,
1.3247663938746845, 0, 0
],
[
4, 1, 'M', 'OFFT', '_H3_', 0,
2.649532787749369, 0.0157, 0.0267, 0,
1.3247663938746845, 0, 0
],
[
5, 1, 'M', 'OFFT', '_H4_', 0,
2.649532787749369, 0.0157, 0.0267, 0,
1.3247663938746845, 0, 0
]]
expected_bonds = [[1, 2, 376.8940758588, 1.094223427522],
[1, 3, 376.8940758588, 1.094223427522],
[1, 4, 376.8940758588, 1.094223427522],
[1, 5, 376.8940758588, 1.094223427522]]
expected_angles = [[2, 1, 3, 33.78875634641, 110.2468561538],
[2, 1, 4, 33.78875634641, 110.2468561538],
[2, 1, 5, 33.78875634641, 110.2468561538],
[3, 1, 4, 33.78875634641, 110.2468561538],
[3, 1, 5, 33.78875634641, 110.2468561538],
[4, 1, 5, 33.78875634641, 110.2468561538]]
check_parameters()
# Second check
molecule.add_OPLS_nonbonding_params()
expected_nonbonding = [[
1, 0, 'M', 'CT', '_C1_', 0, 3.5, 0.066, -0.1088, 1.975, 1.75,
0.005, -0.74168571
],
[
2, 1, 'M', 'HC', '_H1_', 0, 2.5, 0.03,
0.0267, 1.425, 1.25, 0.00859824, 0.268726247
],
[
3, 1, 'M', 'HC', '_H2_', 0, 2.5, 0.03,
0.0267, 1.425, 1.25, 0.00859824, 0.268726247
],
[
4, 1, 'M', 'HC', '_H3_', 0, 2.5, 0.03,
0.0267, 1.425, 1.25, 0.00859824, 0.268726247
],
[
5, 1, 'M', 'HC', '_H4_', 0, 2.5, 0.03,
0.0267, 1.425, 1.25, 0.00859824, 0.268726247
]]
check_parameters()
# Third check
molecule.add_OPLS_bonds_and_angles()
expected_bonds = [[1, 2, 340.0, 1.09], [1, 3, 340.0, 1.09],
[1, 4, 340.0, 1.09], [1, 5, 340.0, 1.09]]
expected_angles = [[2, 1, 3, 33.0, 107.8], [2, 1, 4, 33.0, 107.8],
[2, 1, 5, 33.0, 107.8], [3, 1, 4, 33.0, 107.8],
[3, 1, 5, 33.0, 107.8], [4, 1, 5, 33.0, 107.8]]
check_parameters()